feat: cache submissions in s3 (#1035)

* api to update submission in cache in s3

* feat: api to download submission from cache

* transition from POST to GET for download submission from cache endpoint

* added submissions in a zip file as a sozip file in s3

* added sozipfile module

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* feat: postgis func to convert geojson to flatgeobuf

* docs: extra comments for geosjon_to_flatgeobuf

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* build: recrease pdm.lock with sozipfile

* fix: replace all instances of zipfile with sozipfile

* added metadata json file alongside submission.json in s3 bucket

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* refactor: rename submissions crud functions for clarity

* refactor: simplify update_submission_in_s3

* refactor: reorder submission logic to check for last_submission

* check the last submission date from submission in s3 and compare with submission from odk

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fix:submission path

* update submission download logic with passing task_id as a parameter

* remove: download submission from cache endpoint

* updated parameter task_id to background_task_id

* updated endpoint name

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* updated get data from metadata json

* metadata json added outside of zipfile in s3 bucket

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* refactor: reuse metadata_s3_path variable in submission upload

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: spwoodcock <sam.woodcock@protonmail.com>

src/backend/app/db/postgis_utils.py

@@ -21,8 +21,11 @@
 
 from geoalchemy2 import Geometry
 from geoalchemy2.shape import to_shape
+from geojson import FeatureCollection
 from geojson_pydantic import Feature
 from shapely.geometry import mapping
+from sqlalchemy import text
+from sqlalchemy.orm import Session
 
 
 def timestamp():
@@ -61,3 +64,36 @@ def get_centroid(geometry: Geometry, properties: str = {}, id: int = None):
         }
         return Feature(**geojson)
     return {}
+
+
+def geojson_to_flatgeobuf(db: Session, geojson: FeatureCollection):
+    """From a given FeatureCollection, return a memory flatgeobuf obj."""
+    sql = f"""
+        DROP TABLE IF EXISTS public.temp_features CASCADE;
+
+        CREATE TABLE IF NOT EXISTS public.temp_features(
+            id serial PRIMARY KEY,
+            geom geometry
+        );
+
+        WITH data AS (SELECT '{geojson}'::json AS fc)
+        INSERT INTO public.temp_features (geom)
+        SELECT
+            ST_AsText(ST_GeomFromGeoJSON(feat->>'geometry')) AS geom
+        FROM (
+            SELECT json_array_elements(fc->'features') AS feat
+            FROM data
+        ) AS f;
+
+        WITH thegeom AS
+        (SELECT * FROM public.temp_features)
+        SELECT ST_AsFlatGeobuf(thegeom.*)
+        FROM thegeom;
+    """
+    # Run the SQL
+    result = db.execute(text(sql))
+    # Get a memoryview object, then extract to Bytes
+    flatgeobuf = result.fetchone()[0].tobytes()
+    # Cleanup table
+    db.execute(text("DROP TABLE IF EXISTS public.temp_features CASCADE;"))
+    return flatgeobuf

src/backend/app/projects/project_crud.py

@@ -22,19 +22,18 @@
 import os
 import time
 import uuid
-import zipfile
 from asyncio import gather
 from concurrent.futures import ThreadPoolExecutor, wait
 from io import BytesIO
 from typing import List, Optional, Union
-from zipfile import ZipFile
 
 import geoalchemy2
 import geojson
 import pkg_resources
 import requests
 import segno
 import shapely.wkb as wkblib
+import sozipfile.sozipfile as zipfile
 import sqlalchemy
 from asgiref.sync import async_to_sync
 from fastapi import File, HTTPException, UploadFile
@@ -764,7 +763,7 @@ async def update_project_with_zip(
             detail=f"File must be a zip. Uploaded file was {uploaded_zip.content_type}",
         )
 
-    with ZipFile(io.BytesIO(uploaded_zip.file.read()), "r") as zip:
+    with zipfile.ZipFile(io.BytesIO(uploaded_zip.file.read()), "r") as zip:
         # verify valid zip file
         bad_file = zip.testzip()
         if bad_file:

src/backend/app/submission/submission_crud.py

@@ -21,19 +21,25 @@
 import json
 import os
 import threading
-import zipfile
+import uuid
 from asyncio import gather
+from datetime import datetime
+from io import BytesIO
 from pathlib import Path
 
+import sozipfile.sozipfile as zipfile
 from asgiref.sync import async_to_sync
 from fastapi import HTTPException, Response
 from fastapi.responses import FileResponse
 from loguru import logger as log
 from osm_fieldwork.json2osm import JsonDump
 from sqlalchemy.orm import Session
 
-from ..central.central_crud import get_odk_form, get_odk_project
-from ..projects import project_crud, project_schemas
+from app.central.central_crud import get_odk_form, get_odk_project, list_odk_xforms
+from app.config import settings
+from app.projects import project_crud, project_schemas
+from app.s3 import add_obj_to_bucket, get_obj_from_bucket
+from app.tasks import tasks_crud
 
 
 def get_submission_of_project(db: Session, project_id: int, task_id: int = None):
@@ -300,7 +306,7 @@ def convert_to_osm(db: Session, project_id: int, task_id: int):
         submission = xform.getSubmissions(odkid, task_id, None, False, True)
         submission = (json.loads(submission))["value"]
     else:
-        submission = get_all_submissions(db, project_id)
+        submission = get_all_submissions_json(db, project_id)
 
     if not submission:
         raise HTTPException(status_code=404, detail="Submission not found")
@@ -342,8 +348,12 @@ def convert_to_osm(db: Session, project_id: int, task_id: int):
     return FileResponse(final_zip_file_path)
 
 
-def download_submission_for_project(db, project_id):
-    log.info(f"Downloading all submissions for a project {project_id}")
+def gather_all_submission_csvs(db, project_id):
+    """Gather all of the submission CSVs for a project.
+
+    Generate a single zip with all submissions.
+    """
+    log.info(f"Downloading all CSV submissions for project {project_id}")
 
     get_project_sync = async_to_sync(project_crud.get_project)
     project_info = get_project_sync(db, project_id)
@@ -436,7 +446,103 @@ def extract_files(zip_file_path):
     return final_zip_file_path
 
 
-def get_all_submissions(db: Session, project_id):
+def update_submission_in_s3(
+    db: Session, project_id: int, background_task_id: uuid.UUID
+):
+    try:
+        # Get Project
+        get_project_sync = async_to_sync(project_crud.get_project)
+        project = get_project_sync(db, project_id)
+
+        # Gather metadata
+        odk_credentials = project_schemas.ODKCentral(
+            odk_central_url=project.odk_central_url,
+            odk_central_user=project.odk_central_user,
+            odk_central_password=project.odk_central_password,
+        )
+        odk_forms = list_odk_xforms(project.odkid, odk_credentials, True)
+
+        # Get latest submission date
+        valid_datetimes = [
+            form["lastSubmission"]
+            for form in odk_forms
+            if form["lastSubmission"] is not None
+        ]
+        last_submission = max(
+            valid_datetimes, key=lambda x: datetime.strptime(x, "%Y-%m-%dT%H:%M:%S.%fZ")
+        )
+
+        # Check if the file already exists in s3
+        s3_project_path = f"/{project.organisation_id}/{project_id}"
+        metadata_s3_path = f"/{s3_project_path}/submissions.meta.json"
+        try:
+            # Get the last submission date from the metadata
+            file = get_obj_from_bucket(settings.S3_BUCKET_NAME, metadata_s3_path)
+            zip_file_last_submission = (json.loads(file.getvalue()))["last_submission"]
+            if last_submission <= zip_file_last_submission:
+                # Update background task status to COMPLETED
+                update_bg_task_sync = async_to_sync(
+                    project_crud.update_background_task_status_in_database
+                )
+                update_bg_task_sync(db, background_task_id, 4)  # 4 is COMPLETED
+                return
+
+        except Exception as e:
+            log.warning(str(e))
+            pass
+
+        # Zip file is outdated, regenerate
+        metadata = {
+            "last_submission": last_submission,
+        }
+
+        # Get submissions from ODK Central
+        submissions = get_all_submissions_json(db, project_id)
+
+        submissions_zip = BytesIO()
+        # Create a sozipfile with metadata and submissions
+        with zipfile.ZipFile(
+            submissions_zip,
+            "w",
+            compression=zipfile.ZIP_DEFLATED,
+            chunk_size=zipfile.SOZIP_DEFAULT_CHUNK_SIZE,
+        ) as myzip:
+            myzip.writestr("submissions.json", json.dumps(submissions))
+
+        # Add zipfile to the s3 bucket
+        add_obj_to_bucket(
+            settings.S3_BUCKET_NAME,
+            submissions_zip,
+            f"/{s3_project_path}/submission.zip",
+        )
+
+        # Upload metadata to s3
+        metadata_obj = BytesIO(json.dumps(metadata).encode())
+        add_obj_to_bucket(
+            settings.S3_BUCKET_NAME,
+            metadata_obj,
+            metadata_s3_path,
+        )
+
+        # Update background task status to COMPLETED
+        update_bg_task_sync = async_to_sync(
+            project_crud.update_background_task_status_in_database
+        )
+        update_bg_task_sync(db, background_task_id, 4)  # 4 is COMPLETED
+
+        return True
+
+    except Exception as e:
+        log.warning(str(e))
+        # Update background task status to FAILED
+        update_bg_task_sync = async_to_sync(
+            project_crud.update_background_task_status_in_database
+        )
+        update_bg_task_sync(db, background_task_id, 2, str(e))  # 2 is FAILED
+
+
+def get_all_submissions_json(db: Session, project_id):
+    """Get all submissions for a project in JSON format."""
     get_project_sync = async_to_sync(project_crud.get_project)
     project_info = get_project_sync(db, project_id)
 
@@ -449,9 +555,9 @@ def get_all_submissions(db: Session, project_id):
 
     project = get_odk_project(odk_credentials)
 
-    get_task_id_list_sync = async_to_sync(get_task_id_list)
-    task_lists = get_task_id_list_sync(db, project_id)
-    submissions = project.getAllSubmissions(project_info.odkid, task_lists)
+    get_task_id_list_sync = async_to_sync(tasks_crud.get_task_id_list)
+    task_list = get_task_id_list_sync(db, project_id)
+    submissions = project.getAllSubmissions(project_info.odkid, task_list)
     return submissions
 
 

src/backend/app/submission/submission_routes.py

@@ -17,16 +17,19 @@
 #
 import json
 import os
+from typing import Optional
 
-from fastapi import APIRouter, Depends, Response
+from fastapi import APIRouter, BackgroundTasks, Depends, Response
 from fastapi.concurrency import run_in_threadpool
-from fastapi.responses import FileResponse
+from fastapi.responses import FileResponse, JSONResponse
 from osm_fieldwork.odk_merge import OdkMerge
 from osm_fieldwork.osmfile import OsmFile
 from sqlalchemy.orm import Session
 
-from ..db import database
-from ..projects import project_crud
+from app.config import settings
+from app.db import database
+from app.projects import project_crud, project_schemas
+
 from . import submission_crud
 
 router = APIRouter(
@@ -104,7 +107,7 @@ async def download_submission(
 
     """
     if not (task_id or export_json):
-        file = submission_crud.download_submission_for_project(db, project_id)
+        file = submission_crud.gather_all_submission_csvs(db, project_id)
         return FileResponse(file)
 
     return await submission_crud.download_submission(
@@ -164,7 +167,7 @@ async def conflate_osm_data(
     # All Submissions JSON
     # NOTE runs in separate thread using run_in_threadpool
     submission = await run_in_threadpool(
-        lambda: submission_crud.get_all_submissions(db, project_id)
+        lambda: submission_crud.get_all_submissions_json(db, project_id)
     )
 
     # Data extracta file
@@ -214,6 +217,51 @@ async def conflate_osm_data(
     return []
 
 
+@router.post("/download-submission")
+async def download_submission_json(
+    background_tasks: BackgroundTasks,
+    project_id: int,
+    background_task_id: Optional[str] = None,
+    db: Session = Depends(database.get_db),
+):
+    # Get Project
+    project = await project_crud.get_project(db, project_id)
+
+    # Return existing export if complete
+    if background_task_id:
+        # Get the backgrund task status
+        task_status, task_message = await project_crud.get_background_task_status(
+            background_task_id, db
+        )
+
+        if task_status != 4:
+            return project_schemas.BackgroundTaskStatus(
+                status=task_status.name, message=task_message or ""
+            )
+
+        bucket_root = f"{settings.S3_DOWNLOAD_ROOT}/{settings.S3_BUCKET_NAME}"
+        return JSONResponse(
+            status_code=200,
+            content=f"{bucket_root}/{project.organisation_id}/{project_id}/submission.zip",
+        )
+
+    # Create task in db and return uuid
+    background_task_id = await project_crud.insert_background_task_into_database(
+        db, "sync_submission", project_id
+    )
+
+    background_tasks.add_task(
+        submission_crud.update_submission_in_s3, db, project_id, background_task_id
+    )
+    return JSONResponse(
+        status_code=200,
+        content={
+            "Message": "Submission update process initiated",
+            "task_id": str(background_task_id),
+        },
+    )
+
+
 @router.get("/get_osm_xml/{project_id}")
 async def get_osm_xml(
     project_id: int,
@@ -229,7 +277,7 @@ async def get_osm_xml(
     # All Submissions JSON
     # NOTE runs in separate thread using run_in_threadpool
     submission = await run_in_threadpool(
-        lambda: submission_crud.get_all_submissions(db, project_id)
+        lambda: submission_crud.get_all_submissions_json(db, project_id)
     )
 
     # Write the submission to a file